The matrix must be in this triangular form
with the secondary structure order
 
H 
E 
C 
T 
G 
S 
B 
3 
X
0
 H E C T G S B 3 X 0

IMPORTANT: '0' is treated as wild character. This means that 
           for '0' the open gap penalty is not increased (on the
           contrary to the other symbols). 

### file example identity matrix (default) ###
### cut below this line ###
10 
0 10 
0 0 10 
0 0 0 10 
0 0 0 0 10 
0 0 0 0 0 10 
0 0 0 0 0 0 10 
0 0 0 0 0 0 0 10 
0 0 0 0 0 0 0 0 10 
0 0 0 0 0 0 0 0 0 10 
0 0 0 0 0 0 0 0 0 0 10 
### file example from Wallqvist et al. Bioinformatics 16:988 (2000) ###
### only H E C are considered ###
### cut below this line ###
2
-15 4 
-4 -4 2 
0 0 0 0 
0 0 0 0 0 
0 0 0 0 0 0 
0 0 0 0 0 0 0 
0 0 0 0 0 0 0 0 
0 0 0 0 0 0 0 0 0 
0 0 0 0 0 0 0 0 0 0 
0 0 0 0 0 0 0 0 0 0 0